package de.jabc.sib.bio.ebi;

import de.jabc.adapter.bio.ebi.Branches;
import de.jabc.adapter.bio.ebi.LightweightServiceAdapter;
import de.jabc.adapter.bio.ebi.ServiceAdapter;
import de.metaframe.jabc.framework.execution.ExecutionEnvironment;
import de.metaframe.jabc.framework.sib.annotation.SIBClass;
import de.metaframe.jabc.framework.sib.annotation.SIBStatus;
import de.metaframe.jabc.framework.sib.parameter.ContextExpression;
import de.metaframe.jabc.framework.sib.parameter.ContextKey;
import de.metaframe.jabc.sib.ServiceAdapterDescriptor;

/**
 * Calls the EBI's NCBI BLAST service.
 * 
 * @author anna-lena
 * @version $Revision: 3325 $ $Date: 2008-03-03 13:34:38 +0100 (Mon, 03 Mar
 *          2008) $
 */
@SIBClass("ebi-sibs/ClustalW2Phylogeny")
@SIBStatus("IMPLEMENTED")
public class ClustalW2Phylogeny extends AbstractSIB {

	/* Branches */
	public static final String[] BRANCHES = { Branches.DEFAULT, Branches.ERROR };

	/* Parameters */
	public ContextExpression Email = new ContextExpression("", String.class,
			false);
	public ContextExpression Title = new ContextExpression("", String.class,
			false);
	public ContextExpression Tree = new ContextExpression("", String.class,
			false);
	public ContextExpression Kimura = new ContextExpression("", String.class,
			false);
	public ContextExpression Tossgaps = new ContextExpression("",
			String.class, false);
	public ContextExpression Clustering = new ContextExpression("", String.class,
			false);
	public ContextExpression Pim = new ContextExpression("", String.class,
			false);
	public ContextExpression Sequence = new ContextExpression("", String.class,
			false);
	public ContextKey resultOut = new ContextKey("result_out", ContextKey.Scope.LOCAL,
			true);
	public ContextKey resultSequence = new ContextKey("result_sequence", ContextKey.Scope.LOCAL,
			true);
	public ContextKey resultTree = new ContextKey("result_tree", ContextKey.Scope.LOCAL,
			true);

	
	/**
	 * @see de.metaframe.jabc.sib.CodeGeneratorBlock#execute(ExecutionEnvironment)
	 */
	public String execute(ExecutionEnvironment environment) {
		try {
			return ServiceAdapter.callClustalwPhylogeny(environment, this.Email,
					this.Title, this.Tree, this.Kimura, this.Tossgaps, this.Clustering, this.Pim, this.Sequence, this.resultOut,
					this.resultSequence, this.resultTree);
		} catch (NoClassDefFoundError e) {
			return Branches.ERROR;
		}
	}

	/**
	 * @see de.metaframe.jabc.sib.Generatable#generate()
	 */
	public ServiceAdapterDescriptor generate() {
		return new ServiceAdapterDescriptor(LightweightServiceAdapter.class
				.getName(), "callClustalwPhylogeny", "Email", "Title", "Tree", "Kimura", "Tossgaps", "Clustering", 
				"Pim", "Sequence", "resultOut", "resultSequence", "resultTree");
	}

}
